Sheryl Davis was the former Human Rights Commission Executive Director. James Spingola was the former head of the nonprofit Collective Impact.
The charges against them came after an 18-month long investigation into alleged misuse of public funds that were tied to millions of dollars in city contracts.
Prosecutors allege Davis directed more than $4.5 million in city funds to Collective Impact while maintaining financial ties to the organization.
Davis also allegedly approved millions in city funding to a San Francisco non-profit while the group paid nearly $140,000 to her son.
She is also accused of failing to disclose gifts, improperly using discretionary funds, and facilitating the purchase of copies of a book she authored by the San Francisco Public Library.
Davis faces more than a dozen felony counts and two misdemeanor ethics-related violations. Spingola faces four felony count.
Davis and Spignola surrendered Monday morning on arrest warrants and were booked into San Francisco County jail. Arraignment dates have not yet been announced.